One uses these lines to address someone whom we badly miss when we are away from him or her. The distance and separation from your beloved and the craving to be with them is what makes us weak and makes us miss the person whom we love. When you say "I miss you" to someone, that implies that you are actually missing a person and long for their presence in your life. "I miss you" is a way to show someone that you miss them immensely and also to show them that you are concerned about them.
But don't say "I miss you" someone that often that he starts taking you for granted or becomes irritated because of the frequency with which you occur these words. Don't show someone that you cannot do without their presence. Try keeping yourself happy and calm even in your beloved's absence. Regular utterance of "I miss you" will only weaken you.